Investigative journalists working out of Washington and Islamabad are making claims of secret collaborations between the CIA and Pakistan's Inter-Services Intelligence (ISI) spy agency as part of a covert drone war against militants.

The reports quote classified U.S. intelligence documents as well as officials in Washington and Islamabad.

They say the CIA and Pakistan's ISI have been working together covertly for nearly a decade to carry out air strikes against militant leaders and fighters in Pakistan's tribal regions.

To be sure, there have been hundreds of drone strikes in Pakistan since 2004.

Thousands of people are reported to have been killed, including Pakistani and Afghan Taliban insurgents as well Al-Qaeda-affiliated militants -- Arabs, Chechens, Uzbeks, and other foreign fighters.

But hundreds of civilians in Pakistan's tribal regions have also reportedly been killed by U.S. drone strikes.

Jonathan Landay, a Washington-based national security and intelligence reporter for McClatchy newspapers, reports that the secret cooperation was going on at the same time Pakistan's civilian leaders were publicly criticizing U.S. drone strikes as violations of international law and of Pakistan's sovereignty.

Landay says classified U.S. intelligence reports also show that U.S. President Barack Obama's administration has targeted and killed hundreds of suspected lower-level militants in Pakistan's tribal regions -- despite Washington's claims that U.S. drones have only attacked known senior leaders of Al-Qaeda and its allies.

'Back-Room Bargain'

On April 6, Pulitzer Prize-winning "New York Times" journalist Mark Mazzetti reported that there had been a secret deal in 2004 between the CIA and the ISI to kill a Pakistani Taliban ally in South Waziristan.

Mazzetti reported that the CIA agreed to kill Pashtun tribesman and rebel leader Nek Muhammad -- who was considered by Islamabad to be an enemy of the state.

In exchange, Mazzetti's sources explained, the ISI agreed to allow U.S. Predator drones to fly in Pakistani airspace in order to hunt down Al-Qaeda militants.

Mazzetti said the "back-room bargain...is critical to understanding the origins of a covert drone war that began under the [George W.] Bush administration, was embraced and expanded by President Obama, and is now the subject of fierce debate."

Based on interviews with more than a dozen officials in Pakistan and the United States, Mazzetti disclosed the terms of the reported secret deal.

He said the ISI insisted they be allowed to approve each drone strike -- a condition that gave Pakistan tight control over the list of drone targets. The ISI also insisted that U.S. drones would only be allowed to fly over the tribal regions near the border with Afghanistan.

Mazzetti also said the United States agreed it would never acknowledge U.S. drone strikes, allowing Pakistan either to take credit for killing militants or remain silent.

According to Landay, classified U.S. intelligence reports show that the ISI continued to select its own targets for U.S. drone strikes during most of the Bush administration.

In fact, he reported that the CIA had to get advance approval from the ISI before each drone strike until the middle of 2008.

Landay also said that under both the Bush and Obama administrations, the United States provided the ISI with briefings and video footage of drone strikes.

Written by Ron Synovitz based on reports by "The New York Times" and McClatchy Newspapers